Energy minimization is an important goal in implanted BAN communication system design, and cross-layer optimization is an available approach by optimizing parameters in different layers of OSI model, thus, the system could be energy efficient. In many state-of-the-art communication transceivers, RF and analog section can consume more energy compared to the digital part. In this paper, we establish a system level accurate energy consumption model and choose a suitable modulation scheme first; consider an accurate channel model for implanted BAN communication system design; analysis the relationship between PHY parameters and MAC parameters, then, a cross-layer optimization method for energy-efficient design is proposed. Simulation results reveal that adaptive duty cycle to minimize the energy consumption of the implanted BAN communication system is implemented based on accurate energy consumption model and channel model. Simulation results show relationship crossing layers and good performance on energy saving.